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Quasi-species nature and differential gene expression of severe acute respiratory syndrome coronavirus 2 and phylogenetic analysis of a novel Iranian strain
- Source :
- Infection, Genetics and Evolution
- Publication Year :
- 2020
-
Abstract
- A novel coronavirus related to severe acute respiratory syndrome virus, (SARS-CoV-2) is the causal agent of the COVID-19 pandemic. Despite the genetic mutations across the SARS-CoV-2 genome being recently investigated, its transcriptomic genetic polymorphisms at inter-host level and the viral gene expression level based on each Open Reading Frame (ORF) remains unclear. Using available High Throughput Sequencing (HTS) data and based on SARS-CoV-2 infected human transcriptomic data, this study presents a high-resolution map of SARS-CoV-2 single nucleotide polymorphism (SNP) hotspots in a viral population at inter-host level. Four throat swab samples from COVID-19 infected patients were pooled, with RNA-Seq read retrieved from SRA NCBI to detect 21 SNPs and a replacement across the SARS-CoV-2 genomic population. Twenty-two RNA modification sites on viral transcripts were identified that may cause inter-host genetic diversity of this virus. In addition, the canonical genomic RNAs of N ORF showed higher expression in transcriptomic data and reverse transcriptase quantitative PCR compared to other SARS-CoV-2 ORFs, indicating the importance of this ORF in virus replication or other major functions in virus cycle. Phylogenetic and ancestral sequence analyses based on the entire genome revealed that SARS-CoV-2 is possibly derived from a recombination event between SARS-CoV and Bat SARS-like CoV. Ancestor analysis of the isolates from different locations including Iran suggest shared Chinese ancestry. These results propose the importance of potential inter-host level genetic variations to the evolution of SARS-COV-2, and the formation of viral quasi-species. The RNA modifications discovered in this study may cause amino acid sequence changes in polyprotein, spike protein, product of ORF8 and nucleocapsid (N) protein, suggesting further insights to understanding the functional impacts of mutations in the life cycle and pathogenicity of SARS-CoV-2.<br />Highlights • RdRp, S proteins, ORF8, and nucleoprotein (N) of SARS-CoV-2 have undergone mutations at the inter-host level. • SARS-CoV-2 N gene is expressed abundantly during infection comparing to the 5′ terminal genes. • Single nucleotide polymorphisms in SARS-CoV-2 at Inter-host level cause amino acid changes in the virus genome. • Ancestor analysis of the SARS-CoV-2 isolates from different locations reveals shared Chinese ancestry.
- Subjects :
- 0301 basic medicine
Microbiology (medical)
Gene Expression Regulation, Viral
viruses
030106 microbiology
Population
Inter-host
Single-nucleotide polymorphism
Biology
Iran
medicine.disease_cause
Virus Replication
Genome
Microbiology
Polymorphism, Single Nucleotide
DNA sequencing
Virus
03 medical and health sciences
Phylogenetic
Viral Proteins
Genetic variation
medicine
Genetics
Humans
education
skin and connective tissue diseases
Nucleocapsid
Molecular Biology
Ecology, Evolution, Behavior and Systematics
Phylogeny
Coronavirus
education.field_of_study
SARS-CoV-2
Sequence Analysis, RNA
Gene Expression Profiling
COVID-19
High-Throughput Nucleotide Sequencing
Open reading frame
Single nucleotide polymorphism
body regions
Quasispecies
030104 developmental biology
Infectious Diseases
Pharynx
Research Paper
Subjects
Details
- ISSN :
- 15677257
- Volume :
- 85
- Database :
- OpenAIRE
- Journal :
- Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases
- Accession number :
- edsair.doi.dedup.....118e057b42e483ae326a6379287523b0